| Previous changeset 0:33c060ec0ac9 (2020-10-19) Next changeset 2:96f74538896e (2021-10-19) |
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Commit message:
"planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871" |
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modified:
rna_quast.xml |
| b |
| diff -r 33c060ec0ac9 -r e989670c7fc7 rna_quast.xml --- a/rna_quast.xml Mon Oct 19 08:04:52 2020 +0000 +++ b/rna_quast.xml Thu Feb 18 09:32:20 2021 +0000 |
| [ |
| b'@@ -1,70 +1,82 @@\n <tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@">\n <description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description>\n <macros>\n- <token name="@TOOL_VERSION@">2.1.0</token>\n+ <token name="@TOOL_VERSION@">2.2.0</token>\n <xml name="element_matching_line" token_name="" token_expression="">\n <element name="@NAME@">\n- <assert_contents><has_line_matching expression="@EXPRESSION@"/></assert_contents>\n+ <assert_contents>\n+ <has_line_matching expression="@EXPRESSION@" />\n+ </assert_contents>\n </element>\n </xml>\n <xml name="element_has_text" token_name="" token_text="">\n <element name="@NAME@">\n- <assert_contents><has_text text="@TEXT@"/></assert_contents>\n+ <assert_contents>\n+ <has_text text="@TEXT@" />\n+ </assert_contents>\n </element>\n </xml>\n \n <xml name="details_output_test" token_assembler="">\n <element name="@ASSEMBLER@">\n- <element name="5000%-assembled.list"><assert_contents><has_n_lines n="0"/></assert_contents></element>\n- <element name="9500%-assembled.list"><assert_contents><has_n_lines n="0"/></assert_contents></element>\n- <expand macro="element_matching_line" name="alignment_metrics" expression="\\s*== ALIGNMENT METRICS \\(calculated with reference genome but without gene database\\) ==\\s*"/>\n- <expand macro="element_matching_line" name="alignment_multiplicity" expression="unaligned=\\d+ aligned=\\d+ alignments=\\d+\\s*"/>\n- <expand macro="element_matching_line" name="alignments_per_isoform" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="basic_metrics" expression="\\s*== BASIC TRANSCRIPTS METRICS \\(calculated without reference genome and gene database\\) ==\\s*"/>\n- <expand macro="element_matching_line" name="block_length" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="blocks_per_alignment" expression="avg=[\\d.]+\\s+tot=\\d+\\s*"/>\n- <expand macro="element_matching_line" name="database_metrics" expression="\\s*== GENE DATABASE METRICS ==\\s*"/>\n- <expand macro="element_matching_line" name="misassemblies" expression="\\s*== ALIGNMENT METRICS FOR MISASSEMBLED \\(CHIMERIC\\) TRANSCRIPTS \\(calculated with reference genome or with gene database\\) ==\\s*"/>\n- <expand macro="element_matching_line" name="mismatch_rate" expression="avg=[\\d.]+\\s+tot=\\d+\\s*"/>\n- <expand macro="element_matching_line" name="sensitivity" expression="\\s*== ASSEMBLY COMPLETENESS \\(SENSITIVITY\\) ==\\s*"/>\n- <expand macro="element_matching_line" name="specificity" expression="\\s*== ASSEMBLY SPECIFICITY ==\\s*"/>\n- <expand macro="element_matching_line" name="transcript_length" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="x-aligned" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="x-assembled" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="x-assembled_exons" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="x-covered" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="x-covered_exons" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="x-matched" expression="avg=[\\d.]+\\s*"/>\n- <expand macro="element_matching_line" name="x-matched_blocks" expression="avg=[\\d.]+\\s*"/>\n+ <element name="5000%-assembled.list">\n+ <assert_contents>\n+ <has_n_lines n="0" />\n+ </assert_contents>\n+ </'..b'add</filter>\n </collection>\n </outputs>\n@@ -228,20 +240,20 @@\n <conditional name="gene_coordinates">\n <param name="use_gtf" value="true" />\n <param name="gtf" value="Saccharomyces_cerevisiae.R64-1-1.75.gtf" ftype="gtf" />\n- <param name="disable_infer_genes" value="true"/>\n- <param name="disable_infer_transcripts" value="true"/>\n+ <param name="disable_infer_genes" value="true" />\n+ <param name="disable_infer_transcripts" value="true" />\n </conditional>\n <param name="out_sr" value="txt,tex,tsv" />\n <param name="out_add" value="logs,comparison,plots,details" />\n- <expand macro="txt_output_test"/>\n- <expand macro="tex_output_test"/>\n- <expand macro="tsv_output_test"/>\n- <output_collection name="comparison_png" type="list" count="15"/>\n- <output_collection name="comparison" type="list" count="19"/>\n- <output_collection name="list_logs" type="list" count="8"/>\n+ <expand macro="txt_output_test" />\n+ <expand macro="tex_output_test" />\n+ <expand macro="tsv_output_test" />\n+ <output_collection name="comparison_png" type="list" count="15" />\n+ <output_collection name="comparison" type="list" count="19" />\n+ <output_collection name="list_logs" type="list" count="8" />\n <output_collection name="details" type="list:list" count="2">\n- <expand macro="details_output_test" assembler="Trinity"/>\n- <expand macro="details_output_test" assembler="idba"/>\n+ <expand macro="details_output_test" assembler="Trinity" />\n+ <expand macro="details_output_test" assembler="idba" />\n </output_collection>\n </test>\n <test expect_num_outputs="6">\n@@ -251,22 +263,22 @@\n </conditional>\n <param name="min_alignment" value="30" />\n <param name="lower_threshold" value="45" />\n- <param name="upper_threshold" value="95"/>\n+ <param name="upper_threshold" value="95" />\n <param name="out_sr" value="txt,tex,tsv,pdf" />\n <param name="out_add" value="logs,details_plots" />\n \n- <expand macro="pdf_output_test"/>\n- <expand macro="tex_output_test"/>\n- <expand macro="tsv_output_test"/>\n- <expand macro="txt_output_test"/>\n+ <expand macro="pdf_output_test" />\n+ <expand macro="tex_output_test" />\n+ <expand macro="tsv_output_test" />\n+ <expand macro="txt_output_test" />\n <output_collection name="list_logs" type="list">\n- <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text=""/>\n- <expand macro="element_matching_line" name="rnaQUAST" expression="Thank you for using rnaQUAST!"/>\n+ <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text="" />\n+ <expand macro="element_matching_line" name="rnaQUAST" expression="Thank you for using rnaQUAST!" />\n </output_collection>\n <output_collection name="details_png" type="list:list" count="1">\n <element name="Trinity">\n- <expand macro="element_has_text" name="Nx" text="PNG"/>\n- <expand macro="element_has_text" name="transcript_length" text="PNG"/>\n+ <expand macro="element_has_text" name="Nx" text="PNG" />\n+ <expand macro="element_has_text" name="transcript_length" text="PNG" />\n </element>\n </output_collection>\n </test>\n@@ -325,7 +337,7 @@\n - Database Metrics\n - Alignment multiplicity\n More informations, see citations.\n- ]]></help>\n+ ]]> </help>\n <citations>\n <citation type="doi">10.1093/bioinformatics/btw218 </citation>\n </citations>\n' |